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pyproject.toml
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pyproject.toml
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[build-system]
build-backend = "setuptools.build_meta"
requires = [ "setuptools>=64", "setuptools-scm>=8" ]
[tool.poetry]
name = "CytoDataFrame"
version = "0.0.0"
description = "An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks."
authors = [ "Way Science Community" ]
license = "BSD-3-Clause"
readme = "README.md"
packages = [ { include = "cytodataframe", from = "src" } ]
[tool.poetry.dependencies]
python = ">=3.9,<3.13"
# used for data management
pandas = [
{ version = "<2.2.2", python = "<3.9" },
{ version = "^2.2.2", python = ">=3.9" },
]
# used for data ingest and export
pyarrow = ">=16,<19"
# used for report generation capabilities
plotly = "^5.24.1"
# used for plotly dependencies
kaleido = "0.2.1"
# used for environment detection
ipython = "^8.12.3"
# used for image processing
scikit-image = [
{ version = "^0.19.3", python = "<3.9" },
{ version = ">0.19.3", python = ">=3.9" },
]
# dependency of scikit-image
pywavelets = [
{ version = "^1.4.1", python = "<3.9" },
{ version = ">1.4.1", python = ">=3.9" },
]
# used for image modifications in cytodataframe
opencv-python = "^4.10.0.84"
imagecodecs = "^2024.9.22"
[tool.poetry.group.dev.dependencies]
# provides testing capabilities for project
pytest = "^8.3.3"
# used for report html export to image for tests
html2image = "^2.0.5"
# used for test data generation
sqlalchemy = ">=1.3.6,<3"
# added to generate test coverage reports
coverage = "^7.6.0"
jupyterlab = "^4.3.0"
jupytext = "^1.16.4"
black = "^24.10.0"
isort = "^5.13.2"
jupyterlab-code-formatter = "^3.0.2"
duckdb = "^1.1.3"
[tool.poetry.group.docs.dependencies]
# used for rendering docs into docsite
sphinx = "^7.0.0"
# used for rendering markdown through sphinx
myst-parser = "^3.0.0"
# used for rendering notebooks through myst parser
myst-nb = "^1.1.2"
# used for extension sphinx-multiversion and to fix git-based challenges with default branch handling
sphinx-multiversion = { git = "https://github.com/J-RN/sphinx-multiversion", rev = "a77f0c862dace3a62c18fc866da60ef7dde3873d" }
# used for gathering version data for docsite
dunamai = "^1.22.0"
# used for theming the docsite
pydata-sphinx-theme = "^0.16.0"
[tool.poetry-dynamic-versioning]
enable = true
style = "pep440"
vcs = "git"
[tool.poetry-dynamic-versioning.substitution]
files = [ "src/CytoDataFrame/__init__.py" ]
# defines various development tasks
[tool.setuptools_scm]
root = "."
[tool.ruff]
target-version = "py38"
line-length = 88
fix = true
lint.select = [
# flake8-builtins
"A",
# flake8-annotations
"ANN",
# flake8-comprehensions
"C4",
# mccabe
"C90",
# pycodestyle
"E",
# pyflakes
"F",
# isort
"I",
# pylint
"PL",
# ruff
"RUF",
# flake8-simplify
"SIM",
"W",
]
# Ignore `E402` and `F401` (unused imports) in all `__init__.py` files
lint.per-file-ignores."__init__.py" = [ "E402", "F401" ]
# ignore typing rules for tests
lint.per-file-ignores."tests/*" = [ "ANN201", "PLR0913", "PLR2004" ]
[tool.pytest.ini_options]
markers = [
"generate_report_image: tests which involve the creation of report images.",
]
[tool.coverage.run]
# settings to avoid errors with cv2 and coverage
# see here for more: https://github.com/nedbat/coveragepy/issues/1653
omit = [
"config.py",
"config-3.py",
]
[tool.jupytext]
formats = "ipynb,py:light"
# specify where version replacement is performed
[tool.bandit]
exclude_dirs = [ "tests" ]